Contacts of the helix formed by residues 474 - 479 (chain A) in PDB entry 2W93
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A ILE* 4.9 1.1 - - + -
445A GLY* 3.5 21.6 + - - -
448A GLN* 5.0 2.9 + - - -
449A LEU* 4.8 5.5 - - - +
473A GLY* 1.3 73.2 - - - -
475A THR* 1.3 62.9 + - - +
476A ILE 3.4 2.2 - - - -
477A GLN* 3.2 17.4 + - + +
478A LYS* 3.1 24.2 + - - +
487A TYR 3.4 26.7 - - - -
488A ASN* 2.9 26.0 + - - +
489A GLU 4.9 0.7 - - - -
490A ILE* 3.5 25.1 - - + +
600A TPP 3.3 44.0 - - + -
25B LEU* 3.9 20.0 - - + +
26B PRO* 3.6 15.6 - - + +
48B ASN 4.5 6.1 + - - -
49B ALA* 5.9 0.2 - - - -
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Residues in contact with THR 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A THR* 4.0 5.0 - - - +
471A ASN* 3.1 41.3 - - + +
473A GLY 4.1 2.0 - - - +
474A TYR* 1.3 72.8 - - - +
476A ILE* 1.3 64.1 + - - +
478A LYS* 3.0 7.8 + - + +
479A LEU* 3.0 31.4 + - - +
541A PRO 4.7 0.2 - - - +
542A VAL* 2.7 35.1 + - + +
543A PHE* 4.5 0.5 - - - -
544A ASP 3.6 14.2 + - - -
600A TPP 2.9 16.4 + - - -
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Residues in contact with ILE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR* 5.7 2.5 - - + -
389A GLY* 3.8 23.3 - - - +
390A THR* 4.2 3.1 - - - +
393A PHE* 3.5 32.8 - - + -
475A THR* 1.3 76.2 + - - +
477A GLN* 1.3 65.3 + - + +
479A LEU* 3.7 8.4 + - - +
480A ILE* 3.3 27.1 - - + +
549A LEU* 3.9 23.3 - - + +
600A TPP 2.9 57.3 + - + +
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Residues in contact with GLN 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A TYR* 3.2 10.5 + - - +
475A THR 3.1 0.8 - - - -
476A ILE* 1.3 77.0 - - + +
478A LYS* 1.3 61.3 + - - +
479A LEU 3.1 1.8 - - - -
480A ILE* 2.9 11.7 + - + +
481A HIS* 2.8 32.7 + - - +
488A ASN* 2.8 34.3 + - - +
600A TPP 3.2 44.1 + - + +
26B PRO* 3.6 25.7 - - - +
27B GLY* 3.4 21.4 - - - -
28B ASP* 4.4 4.3 + - - +
31B LEU* 4.1 16.7 - - + +
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Residues in contact with LYS 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ASN 4.7 0.2 + - - -
472A ASP 3.0 19.6 + - - -
473A GLY* 4.1 0.6 - - - -
474A TYR 3.1 21.1 + - - +
475A THR* 3.0 10.9 + - - +
477A GLN* 1.3 77.2 - - - +
479A LEU* 1.3 61.8 + - - +
480A ILE 3.3 1.2 + - - -
481A HIS 3.8 9.4 + - - -
482A GLY 3.9 0.2 - - - +
483A PRO* 3.5 48.1 + - + +
488A ASN* 3.3 35.4 - - + +
489A GLU* 2.7 35.8 + - - -
542A VAL* 3.6 27.0 - - + +
543A PHE* 4.0 10.7 - - + -
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A THR* 3.0 23.8 + - - +
476A ILE* 3.8 6.7 - - - +
477A GLN 3.1 0.2 - - - -
478A LYS* 1.3 76.8 - - - +
480A ILE* 1.3 60.8 + - + +
543A PHE* 3.7 38.1 - - + +
545A ALA* 3.5 31.6 - - + -
549A LEU* 4.1 24.0 - - + +
550A VAL* 5.2 9.2 - - + -
553A ALA* 4.1 25.4 - - + +
554A LYS* 5.2 2.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il